Contacts of the strand formed by residues 63 - 72 (chain B) in PDB entry 5TX4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 63 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B SER* 3.8 25.8 - - - +
61B GLN 3.7 7.0 + - - +
62B ASP* 1.3 83.5 - - - +
64B GLU* 1.3 68.4 + - - +
65B PRO* 4.8 0.3 - - - +
83B ASN* 3.7 48.0 - - + +
84B MET 5.9 0.4 - - - -
85B ILE 3.1 15.0 - - - +
86B VAL* 3.7 16.8 - - + -
87B LYS* 4.4 0.4 - - - -
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 1.3 76.6 - - - +
65B PRO* 1.3 76.6 - - + +
83B ASN 4.2 4.0 - - - -
84B MET 3.1 8.6 + - - -
85B ILE* 2.8 37.9 + - + +
87B LYS* 3.2 51.4 + - + +
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Residues in contact with PRO 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU 4.8 0.7 - - - +
64B GLU* 1.3 99.9 - - + +
66B LEU* 1.3 60.1 + - - +
67B THR 4.2 0.6 + - - -
80B GLN* 3.2 33.4 - - + +
81B LEU 3.1 21.3 - - - +
82B SER* 4.1 9.4 - - - +
84B MET* 4.6 0.2 - - - -
85B ILE* 3.6 13.0 - - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.4 37.2 - - + -
36B PRO* 4.3 9.9 - - + -
39B TYR* 3.6 35.4 - - + -
65B PRO* 1.3 74.5 - - - +
67B THR* 1.3 73.4 + - - +
68B ILE* 3.6 12.1 + - + +
80B GLN* 4.3 1.6 - - - -
81B LEU* 2.9 31.5 + - - +
84B MET* 4.0 20.4 - - + +
85B ILE* 4.5 9.9 - - + -
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PRO* 3.7 13.0 - - - +
65B PRO 4.2 0.6 + - - -
66B LEU* 1.3 80.1 - - - +
68B ILE* 1.3 64.9 + - - +
69B VAL* 6.1 0.7 - - + -
78B VAL* 3.9 23.6 - - + -
79B GLU 3.5 13.0 - - - +
80B GLN* 3.7 20.8 + - + +
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Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TRP* 3.8 17.5 - - + -
33B ILE* 4.2 15.7 - - + -
35B GLU 3.4 11.0 - - - +
36B PRO* 4.2 2.5 - - + -
66B LEU* 3.9 24.0 - - + +
67B THR* 1.3 79.1 - - - +
69B VAL* 1.3 63.2 + - - +
70B TYR* 3.8 27.5 - - + -
77B LYS 3.8 0.3 - - - +
78B VAL* 3.3 9.0 - - - +
79B GLU* 2.8 45.5 + - + +
81B LEU* 3.6 39.0 - - + -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 3.8 2.4 - - - +
34B HIS* 2.8 42.3 + - + -
35B GLU* 2.9 29.5 + - + +
67B THR* 6.1 0.4 - - + -
68B ILE* 1.3 76.3 - - - +
70B TYR* 1.3 68.4 + - - +
71B TYR* 4.7 1.3 - - + -
76B PRO* 4.5 15.3 - - + -
77B LYS 3.2 9.9 - - - +
78B VAL* 4.0 21.3 - - + -
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ILE* 3.8 22.7 - - + -
32B TRP* 3.4 35.9 - + + +
33B ILE* 4.5 0.7 - - - -
34B HIS* 4.1 4.9 - - - +
68B ILE* 3.8 22.9 - - + -
69B VAL* 1.3 76.3 - - - +
71B TYR* 1.3 61.7 + - - +
72B VAL* 3.5 24.9 - - + -
76B PRO* 3.5 1.4 - - - +
77B LYS* 2.7 69.1 + - + +
79B GLU* 3.7 39.4 + - + -
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.6 43.3 - - + +
51A THR 4.3 4.2 + - - +
52A SER* 3.7 14.2 - - - -
53A ILE* 3.0 31.7 + - - +
32B TRP 4.5 2.9 + - - +
34B HIS* 3.7 41.3 + + + -
69B VAL* 4.7 2.2 - - + -
70B TYR* 1.3 79.6 - - - +
72B VAL* 1.3 63.3 + - - +
73B GLY 3.8 8.7 - - - +
74B ARG* 3.7 30.1 - - - -
75B LYS 3.5 2.7 - - - -
76B PRO* 3.7 31.1 - - + +
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ILE* 3.3 21.1 - - + +
54A CYS 4.8 1.1 - - - +
55A GLU* 4.2 21.6 - - + +
70B TYR* 3.5 30.7 + - + -
71B TYR* 1.3 72.4 - - - +
73B GLY* 1.3 67.7 + - - +
75B LYS* 3.0 29.8 + - + +
77B LYS* 4.2 26.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il